Protocol

AlphaProteo expression and HTRF confirmation funnel for yeast-display hits

Counts of yeast-display hits that were selected for E. coli expression, subcloned and expressed, tested by HTRF, and showed HTRF binding.

28 evaluations · 28 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

28 recorded evaluations, 28 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

28 evaluations · 28 results. Different protocols are not a single leaderboard.

Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits

In source order. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Count (Observed HTRF binding)	Count (Successfully subcloned and expressed)	Count (Tested by HTRF)	Count (Yeast surface display hits selected for E. coli expression)
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target BHRF1	2	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-17A	3	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-7RA	11	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target PD-L1	16	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target SC2RBD	14	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target TrkA	5	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target VEGF-A	20	Not reported	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target BHRF1	Not reported	2	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-17A	Not reported	9	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-7RA	Not reported	11	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target PD-L1	Not reported	20	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target SC2RBD	Not reported	17	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target TrkA	Not reported	5	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target VEGF-A	Not reported	31	Not reported	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target BHRF1	Not reported	Not reported	2	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-17A	Not reported	Not reported	7	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-7RA	Not reported	Not reported	11	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target PD-L1	Not reported	Not reported	18	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target SC2RBD	Not reported	Not reported	17	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target TrkA	Not reported	Not reported	5	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target VEGF-A	Not reported	Not reported	31	Not reported
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target BHRF1	Not reported	Not reported	Not reported	2
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-17A	Not reported	Not reported	Not reported	9
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target IL-7RA	Not reported	Not reported	Not reported	11
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target PD-L1	Not reported	Not reported	Not reported	21
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target SC2RBD	Not reported	Not reported	Not reported	18
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target TrkA	Not reported	Not reported	Not reported	10
AlphaProteo, pooled over tested design systemsEvaluation	AlphaProteo binder design target VEGF-A	Not reported	Not reported	Not reported	31

All 28 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target BHRF1	2 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for BHRF1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'BHRF1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-17A	3 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for IL-17A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'IL-17A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-7RA	11 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for IL-7RA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'IL-7RA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target PD-L1	16 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for PD-L1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'PD-L1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target SC2RBD	14 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for SC2RBD (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'SC2RBD'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target TrkA	5 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for TrkA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'TrkA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target VEGF-A	20 Count (Observed HTRF binding) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo observed htrf binding for VEGF-A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Observed HTRF binding', column 'VEGF-A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target BHRF1	2 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for BHRF1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'BHRF1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-17A	9 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for IL-17A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'IL-17A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-7RA	11 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for IL-7RA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'IL-7RA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target PD-L1	20 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for PD-L1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'PD-L1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target SC2RBD	17 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for SC2RBD (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'SC2RBD'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target TrkA	5 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for TrkA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'TrkA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target VEGF-A	31 Count (Successfully subcloned and expressed) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo successfully subcloned and expressed for VEGF-A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Successfully subcloned and expressed', column 'VEGF-A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target BHRF1	2 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for BHRF1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'BHRF1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-17A	7 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for IL-17A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'IL-17A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-7RA	11 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for IL-7RA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'IL-7RA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target PD-L1	18 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for PD-L1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'PD-L1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target SC2RBD	17 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for SC2RBD (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'SC2RBD'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target TrkA	5 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for TrkA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'TrkA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target VEGF-A	31 Count (Tested by HTRF) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo tested by htrf for VEGF-A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Tested by HTRF', column 'VEGF-A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target BHRF1	2 Count (Yeast surface display hits selected for E. coli expression) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo yeast surface display hits selected for e. coli expression for BHRF1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Yeast surface display hits selected for E. coli expression', column 'BHRF1'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-17A	9 Count (Yeast surface display hits selected for E. coli expression) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo yeast surface display hits selected for e. coli expression for IL-17A (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Yeast surface display hits selected for E. coli expression', column 'IL-17A'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target IL-7RA	11 Count (Yeast surface display hits selected for E. coli expression) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo yeast surface display hits selected for e. coli expression for IL-7RA (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Yeast surface display hits selected for E. coli expression', column 'IL-7RA'
Configuration: AlphaProteo, pooled over tested design systems	Protocol: AlphaProteo expression and HTRF confirmation funnel for yeast-display hits Dataset: AlphaProteo binder design target PD-L1	21 Count (Yeast surface display hits selected for E. coli expression) count · unknown Uncertainty: Not applicable: An exact count. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Table S2 prints the RFdiffusion yeast-display success rate for IL-7RA as 16.8% and Table 1 rounds it to 17, but Section S4.1 states it in the text as '16% versus 33%'. Section S4.1 also states TrkA as '0% (versus 6%)' where Table S2 prints 0.0 and 6.3. The table values are recorded; the text rounds down rather than to nearest.De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table 1; Table S2; Section S4.1 Methods, coverage and source AlphaProteo yeast surface display hits selected for e. coli expression for PD-L1 (Table S3) uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel Aggregation: Not reported De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Table S3, row 'Yeast surface display hits selected for E. coli expression', column 'PD-L1'

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De novo design of high-affinity protein binders with AlphaProteo (Zambaldi et al., arXiv 2024) · Original source · arXiv version 1, posted 2024-09-12; full-text PDF (49 pages)

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Technical metadata and extraction receipts

Stable ID: uc-binder-20261022-protocol-alphaproteo-ecoli-htrf-funnel

areas: proteins-complexes; protein-structure
contexts: research
limitations: The number of yeast hits selected for E. coli expression is an author choice, not the full hit set, so these counts do not reconstruct the full funnel from the hit rates.; TNF-alpha has no column in Table S3, consistent with its 0% hit rate.; Developer-reported.
metric: count
metric direction: unknown
metric qualifier: designs surviving each stage of the expression and confirmation funnel
protocol: Yeast hits chosen for follow-up were subcloned and expressed in E. coli, then tested for binding by HTRF. Table S3 reports the count surviving each stage per target.
review: artifact sha256: 953b35644c0fa06ff090d7614c2e19525831f8fde50242e176d54474133c5a42; method: source-hash-verification; independent-cell-check; ai-assisted-source-review; method note: Re-downloaded with curl (HTTP 200, 12,333,400 bytes) and the SHA-256 recomputed and matched. Own text layer made with pdftotext -layout (poppler 26.08.0), reproducing the extraction pass's 2,811 lines. Table 1, Table S2, Table S3 and Sections S1.2.1, S2, S4.1 and S4.2 read cell by cell and compared with every record. Column assignment re-derived arithmetically rather than trusted.; note: Reviewed in docs/reviews/use-cases/binder-2026-10-22.md. Automated AI review of the source transcription only; it is not human scientific review and nothing here was reproduced experimentally.; retrieval url: https://arxiv.org/pdf/2409.08022v1; reviewed at: 2026-10-22T15:00:00Z; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed
source locator: Table S3
unit: count
unit detail: designs
version: arXiv:2409.08022v1 Table S3

Related records

assessment: AlphaProteo observed htrf binding for BHRF1 (Table S3)
assessment: AlphaProteo observed htrf binding for IL-17A (Table S3)
assessment: AlphaProteo observed htrf binding for IL-7RA (Table S3)
assessment: AlphaProteo observed htrf binding for PD-L1 (Table S3)
assessment: AlphaProteo observed htrf binding for SC2RBD (Table S3)
assessment: AlphaProteo observed htrf binding for TrkA (Table S3)
assessment: AlphaProteo observed htrf binding for VEGF-A (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for BHRF1 (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for IL-17A (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for IL-7RA (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for PD-L1 (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for SC2RBD (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for TrkA (Table S3)
assessment: AlphaProteo successfully subcloned and expressed for VEGF-A (Table S3)
assessment: AlphaProteo tested by htrf for BHRF1 (Table S3)
assessment: AlphaProteo tested by htrf for IL-17A (Table S3)
assessment: AlphaProteo tested by htrf for IL-7RA (Table S3)
assessment: AlphaProteo tested by htrf for PD-L1 (Table S3)
assessment: AlphaProteo tested by htrf for SC2RBD (Table S3)
assessment: AlphaProteo tested by htrf for TrkA (Table S3)
assessment: AlphaProteo tested by htrf for VEGF-A (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for BHRF1 (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for IL-17A (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for IL-7RA (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for PD-L1 (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for SC2RBD (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for TrkA (Table S3)
assessment: AlphaProteo yeast surface display hits selected for e. coli expression for VEGF-A (Table S3)
assessed by: Design a new binder to a chosen target

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